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Microbiology 101

Microbiology is the study of microorganisms (microbes), or as some people call them, “germs”. In total, there are thousands upon thousands of different species of microbes, so organizing them is quite difficult. Therefore, scientists have developed 9 levels of classification to differentiate among them. Fortunate for us, you only need to know two of them. Written in order, these are the genus and the species. For example, the infamous microbe Escherichia coli, is simply a species of microorganism called “coli”, found within the Escherichia genus. This method of naming microbes is called “binomial nomenclature“, and is the gold standard for naming microbes.

So how do scientists define a species of microorganism? The truth is, there really isn’t any set system. In fact, microbes get their species designations moved around all the time. Our current working definition of a microbial species is based upon what is known as the 16S rRNA sequence. This is a DNA-like sequence that all microorganisms share, and that they pass on to their offspring. The useful thing about 16S rRNA is that it changes in a predictable, measurable manner, but that’s a complicated story for another rainy day. Anyway, the rule of thumb is that two microbes which display more than 97% similarity in their 16S rRNA sequence are considered to be of the same species. Any two species with more than 97% sequence similarity are considered different strains of the same species.

So why should we care about microorganisms at all? Well, it turns out everyone has their own unique set of microbes living inside them, collectively known as the microbiome. In fact, the different organs inside your body can be identified by which types of microbes are present, meaning each organ has its own unique microbiome. For example, our skin microbiome primarily contains bacteria from the genera Bacillus and Staphylococcus, while our intestinal microbiome primarily contains bacteria from the genus Lactobacillus.

We now know that our microbiome plays a big role in how healthy we are. For example, the presence of certain microbial species (Akkermansia muciniphila, to be exact) in the gut has been linked to a reduction in obesity-related symptoms. However, scientists still have no idea as to what constitutes a healthy, “normal” microbiome because there are many obstacles to overcome when studying the microbiome. For starters, our microbiome changes depending upon what we eat and who we have close contact with. In addition, although many species of microorganisms are known, we have barely scratched the surface. That, and we have no idea how they interact with each other. Therefore, reading our microbiome is like reading a book in a different language, but without knowing the entire alphabet and only knowing a couple complete words!